Literature DB >> 28398311

Nextflow enables reproducible computational workflows.

Paolo Di Tommaso1, Maria Chatzou1,2, Evan W Floden1,2, Pablo Prieto Barja1,2, Emilio Palumbo1, Cedric Notredame1.   

Abstract

Mesh：

Year:  2017        PMID： 28398311     DOI： 10.1038/nbt.3820

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


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  19 in total

1.  Rebooting review.

Authors: 
Journal:  Nat Biotechnol       Date:  2015-04       Impact factor: 54.908

2.  RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.

Authors:  Alexandros Stamatakis
Journal:  Bioinformatics       Date:  2006-08-23       Impact factor: 6.937

3.  Democratic databases: science on GitHub.

Authors:  Jeffrey Perkel
Journal:  Nature       Date:  2016-10-06       Impact factor: 49.962

4.  Near-optimal probabilistic RNA-seq quantification.

Authors:  Nicolas L Bray; Harold Pimentel; Páll Melsted; Lior Pachter
Journal:  Nat Biotechnol       Date:  2016-04-04       Impact factor: 54.908

5.  AlgoRun: a Docker-based packaging system for platform-agnostic implemented algorithms.

Authors:  Abdelrahman Hosny; Paola Vera-Licona; Reinhard Laubenbacher; Thibauld Favre
Journal:  Bioinformatics       Date:  2016-03-02       Impact factor: 6.937

6.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.

Authors:  Jeremy Goecks; Anton Nekrutenko; James Taylor
Journal:  Genome Biol       Date:  2010-08-25       Impact factor: 13.583

7.  RIPOSTE: a framework for improving the design and analysis of laboratory-based research.

Authors:  Nicholas Gd Masca; Elizabeth Ma Hensor; Victoria R Cornelius; Francesca M Buffa; Helen M Marriott; James M Eales; Michael P Messenger; Amy E Anderson; Chris Boot; Catey Bunce; Robert D Goldin; Jessica Harris; Rod F Hinchliffe; Hiba Junaid; Shaun Kingston; Carmen Martin-Ruiz; Christopher P Nelson; Janet Peacock; Paul T Seed; Bethany Shinkins; Karl J Staples; Jamie Toombs; Adam Ka Wright; M Dawn Teare
Journal:  Elife       Date:  2015-05-07       Impact factor: 8.140

8.  Bioboxes: standardised containers for interchangeable bioinformatics software.

Authors:  Peter Belmann; Johannes Dröge; Andreas Bremges; Alice C McHardy; Alexander Sczyrba; Michael D Barton
Journal:  Gigascience       Date:  2015-10-15       Impact factor: 6.524

Review 9.  Tools and techniques for computational reproducibility.

Authors:  Stephen R Piccolo; Michael B Frampton
Journal:  Gigascience       Date:  2016-07-11       Impact factor: 6.524

Review 10.  Translating RNA sequencing into clinical diagnostics: opportunities and challenges.

Authors:  Sara A Byron; Kendall R Van Keuren-Jensen; David M Engelthaler; John D Carpten; David W Craig
Journal:  Nat Rev Genet       Date:  2016-03-21       Impact factor: 53.242
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  345 in total

1.  Fenofibrate prevents skeletal muscle loss in mice with lung cancer.

Authors:  Marcus D Goncalves; Seo-Kyoung Hwang; Chantal Pauli; Charles J Murphy; Zhe Cheng; Benjamin D Hopkins; David Wu; Ryan M Loughran; Brooke M Emerling; Guoan Zhang; Douglas T Fearon; Lewis C Cantley
Journal:  Proc Natl Acad Sci U S A       Date:  2018-01-08       Impact factor: 11.205

2.  Hyperparameter optimization for image analysis: application to prostate tissue images and live cell data of virus-infected cells.

Authors:  Christian Ritter; Thomas Wollmann; Patrick Bernhard; Manuel Gunkel; Delia M Braun; Ji-Young Lee; Jan Meiners; Ronald Simon; Guido Sauter; Holger Erfle; Karsten Rippe; Ralf Bartenschlager; Karl Rohr
Journal:  Int J Comput Assist Radiol Surg       Date:  2019-06-08       Impact factor: 2.924

3.  Tibanna: software for scalable execution of portable pipelines on the cloud.

Authors:  Soohyun Lee; Jeremy Johnson; Carl Vitzthum; Koray Kırlı; Burak H Alver; Peter J Park
Journal:  Bioinformatics       Date:  2019-11-01       Impact factor: 6.937

4.  Identifying high-confidence capture Hi-C interactions using CHiCANE.

Authors:  Erle M Holgersen; Andrea Gillespie; Olivia C Leavy; Joseph S Baxter; Alisa Zvereva; Gareth Muirhead; Nichola Johnson; Orsolya Sipos; Nicola H Dryden; Laura R Broome; Yi Chen; Igor Kozin; Frank Dudbridge; Olivia Fletcher; Syed Haider
Journal:  Nat Protoc       Date:  2021-04-09       Impact factor: 13.491

5.  Needlestack: an ultra-sensitive variant caller for multi-sample next generation sequencing data.

Authors:  Tiffany M Delhomme; Patrice H Avogbe; Aurélie A G Gabriel; Nicolas Alcala; Noemie Leblay; Catherine Voegele; Maxime Vallée; Priscilia Chopard; Amélie Chabrier; Behnoush Abedi-Ardekani; Valérie Gaborieau; Ivana Holcatova; Vladimir Janout; Lenka Foretová; Sasa Milosavljevic; David Zaridze; Anush Mukeriya; Elisabeth Brambilla; Paul Brennan; Ghislaine Scelo; Lynnette Fernandez-Cuesta; Graham Byrnes; Florence L Calvez-Kelm; James D McKay; Matthieu Foll
Journal:  NAR Genom Bioinform       Date:  2020-04-20

6.  MaRe: Processing Big Data with application containers on Apache Spark.

Authors:  Marco Capuccini; Martin Dahlö; Salman Toor; Ola Spjuth
Journal:  Gigascience       Date:  2020-05-01       Impact factor: 6.524

7.  JASS: command line and web interface for the joint analysis of GWAS results.

Authors:  Hanna Julienne; Pierre Lechat; Vincent Guillemot; Carla Lasry; Chunzi Yao; Robinson Araud; Vincent Laville; Bjarni Vilhjalmsson; Hervé Ménager; Hugues Aschard
Journal:  NAR Genom Bioinform       Date:  2020-01-24

Review 8.  Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit.

Authors:  Fernando Meyer; Till-Robin Lesker; David Koslicki; Adrian Fritz; Alexey Gurevich; Aaron E Darling; Alexander Sczyrba; Andreas Bremges; Alice C McHardy
Journal:  Nat Protoc       Date:  2021-03-01       Impact factor: 13.491

9.  Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification.

Authors:  Michael I Love; Charlotte Soneson; Rob Patro
Journal:  F1000Res       Date:  2018-06-27

10.  Unifying package managers, workflow engines, and containers: Computational reproducibility with BioNix.

Authors:  Justin Bedő; Leon Di Stefano; Anthony T Papenfuss
Journal:  Gigascience       Date:  2020-11-18       Impact factor: 6.524
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